The Church "a people brought into unity in the unity of the Father, the Son and the Holy Spirit", is an extension of the Mystery of the incarnation and of the Kingdom of God inaugurated by Jesus Christ on earth and brought about by the mission given to the Apostles (Mt 28:18-20), for proclaiming and establishing, among all peoples, the Kingdom of God. While she slowly grows to maturity, the Church longs for the completed Kingdom. The Church through her presence and mission in the world continues this sanctifying ministry which Her Master initiated.

The Apostles and their successors planted the Church of Christ in various places. In divine providence (LG 23), India was blessed to have an apostolic foundation of the Church, through the evangelization mission of St. Thomas, one of the twelve Apostles of Jesus Christ. St. Thomas first landed at Malliankara (Kodungallur), started his mission in Malankara (also known as Malabar), the southern tip of the Indian peninsula. Because of this apostolic tradition, this Church was then known as the Church of St. Thomas and the ecclesial community that originated from this apostolic tradition was known as "The St. Thomas Christians", or "Malankara Nazranikal" and the head of the Church was known by the title "Metropolitan of All India".

The Church of St. Thomas in India got rooted in the socio-cultural milieu of India and developed her own ecclesial, liturgical, spiritual and administrative traditions. This was in communion with the Universal Church through her ecclesial communion with the Churches of the Middle East. Besides the Metropolitan of all India, there was also a leader of the St. Thomas Christians, a priest with the title, "Archdeacon of all India" who played a vital role in the day-to-day administration of the Church. This Apostolic Church was in Catholic Communion from the very early centuries. It came in contact with the Syro-Chaldean Church of the Middle East and consequently adopted the East Syrian Liturgy.

In the 16th Century, this Apostolic Church came into direct relationship with the Western Church through the Portuguese missionaries. The Portuguese extended the Padroado agreement in their evangelization program over India and wanted to bring the Indian Church of the St. Thomas Christians under this jurisdiction. The Church in India which was rooted in the socio-cultural environment and which enjoyed autonomy in internal administration in communion with the Universal Chruch resisted the unwanted intervention of the Portuguese who brought with them the Western ecclesiastical traditions. The Protuguese missionaries, ignorant of the Oriental traditions of the Indian Church, had the conviction that anything different from the Western Church was schism and heresy. Hence they wanted to latinize the Syrian Christians of India.

In 1599 Archbishop Alexis Menezis convoked a Synod of Diamper (Udayamperoor) and imposed latin practices and ritual traditions on the Apostolic Church of India. This was a blow to the identity of the Indian Church. However, the relation continued till the beginning of the 2nd of the 17th century. The Church of St. Thomas Christians could not withstand any more the denial of her autonomy. The initial resistance slowly gave way to discontentment, which ended up with the revolt in 1653 known as the Koonan Cross Oath. Thus, the one Church of St. Thomas Christians was split into two. A large majority of the broken-away-group hesitated to sever ties with Rome and they remained in communion with Rome, but, under the Latin Hierarchy. This group came to be call the Pazhayakuttukar, while the other was known as Puthenkuttukar. The latter group made several attempts for reunion with Rome safeguarding their autonomy and patrimony. Failing to re-establish communion with Rome, they happened to come in communion with the Jacobite Syrian Church Antioch. These developments were not acts against the Apostolic See of Rome but against the Portuguese missionaries and their policy of latinization. Even after the communion with the Jacobite See of Antioch, the Malankara Prelates Mar Thomas I (+1670), Mar Thomas II (+1686), , Mar Thomas III (+1688), , Mar Thomas IV (+1728), , Mar Thomas V (+1765), , Mar Thomas VI (+1808) and Mar Thomas VII (+1815) one after the other had attempted reunion with the Holy See, but all ended up in failure.

The Puthenkur community came under the influence of the British missionaries in the 19th century. From 1815 till 1856, the year of the Synod of Mavelikara, the British missionaries propagated Protestant ideology among the Puthenkuttukar. This paved the way to the formation of the Mar Thoma Church under the leadership of Palakunnath Abraham Malpan and Mar Athanasios, who was consecrated Bishop by the Patriarch of Antioch. In order to outdo the reformists Mar Divannasios approached the Patriarch of Antioch. Patriarch Peter III arrived in Malankara and in the Synod of Mulanthuruthy (1876) the Malankara Church had to accept the authority of the Patriarch of Antioch over this Church. Since then, the Malanakara Church had contented that the Patriarch's authority was only in spiritual matters.

It was in this contentious context that Patriarch Mar Abdulla who came to Malankara, excommunicated Vattasseril Mar Divannasios in the year 1911. In this